Continuity mistake: In the scene where Flint has been persuaded by the Mayor to keep the machine running and is about to enter the food code, it changes to a shot showing his computer screen. in this shot, his computer is using Windows. But in the shot of the same screen where Flint's Father is about to send him the kill code, the computer is using a Mac OS. (00:45:35 - 01:08:05)
Other mistake: When Sam reports on the Spaghetti tornado, she reports that she is broadcasting from Chew and Swallow. This is the name of the town from the original children's storybook, which was changed to Swallow Falls for the movie. (00:51:10)
Other mistake: In the scene where the mayor is talking behind the chainlink fence, with Brent in the background eating Sardines, you can see as the mayor grabs the fence the fencewire is going through his thumbs. This is on both hands and easily visible.
Continuity mistake: After the spaghetti twister, Flint puts on his lab coat in the elevator and you can see he has his tuxedo shirt on. Then during the building montage, it's a blue shirt, then changes back to the tuxedo shirt when he turns on the car. Also, during the building, the design on the blue shirt disappears.
Continuity mistake: On the dock, in the shot of the clouds, you can see about 100 hamburgers aimed for the dock (the middle). Yet at the end of the scene when Flint says, "It really works!" only 20 or so hamburgers are visible on the dock. The wind was moving south as seen by Flint's coat blowing in the breeze, so the wind couldn't have blown them in the water. Also, the fact that we see one more shot of the clouds and the burgers (with about 200 more aiming for the dock) makes this impossible.
Other mistake: When Flint configures the computer to rain breakfast, he types the eggs as "over easy". However, when breakfast falls, all of the eggs are sunny side up. This is not likely an error of his invention because in every other case it produces the food exactly as he inputs it.
Plot hole: When Flint gets to his lab to shut down the machine he finds the mayor there inputting more food. The mayor says he's been ordering food for ten minutes, how is this possible when he was just there with Flint on the stage barely a minute or so before? Also, how did the mayor manage to get his large self back to Flint's lab so quickly?
Continuity mistake: In the beginning no-one's shoes are untied, then it shows you they are, and after that they're tied again.
Revealing mistake: When Flint screws the fuse into the fuse box to get the lights back on his dad just appears out of thin air.